DNA encoding SPNF of the spinosyn cluster

ABSTRACT

Spinosyn biosynthetic genes from  Saccharopolyspora spinosa,  spinosyn producing microorganisms transformed with the biosynthetic genes, methods using the biosynthetic genes to increase production of spinosyn insecticidal macrolides, and methods using the genes or fragments thereof to change the products produced by spinosyn-producing microorganisms are provided.

This application is a divisional of application Ser. No. 09/603,207, filed Jun. 23, 2000, U.S. Pat. No. 6,521,406, which is is a divisional of application Ser. No. 09/370,700, filed Aug. 9, 1999, U.S. Pat. No. 6,274,350, which is a divisional of application Ser. No. 09/036,987, filed Mar. 9, 1998, U.S. Pat. No. 6,143,526.

SUMMARY OF THE INVENTION

The present invention provides novel biosynthetic genes, vectors incorporating the biosynthetic genes, Saccharopolyspora spinosa strains transformed with the biosynthetic genes, methods using these genes to increase production of spinosyn insecticidal macrolides, and methods using the genes or fragments thereof to change the products produced by spinosyn-producing strains of Saccharopolyspora spinosa.

BACKGROUND OF THE INVENTION

As disclosed in U.S. Pat. No. 5,362,634, fermentation product A83543 is a family of related compounds produced by Saccharopolyspora spinosa. The known members of this family have been referred to as factors or components, and each has been given an identifying letter designation. These compounds are hereinafter referred to as spinosyn A, B, etc. The spinosyn compounds are useful for the control of arachnids, nematodes and insects, in particular Lepidoptera and Diptera species, and they are quite environmentally friendly and have an appealing toxicological profile. Tables 1 and 2 identify the structures of a variety of known spinosyn compounds:

TABLE 1

Factor R^(1′) R^(2′) R^(3′) R^(4′) R^(5′) R^(6′) R^(7′) spinosyn A H CH₃

C₂H₅ CH₃ CH₃ CH₃ (a) spinosyn B H CH₃

C₂H₅ CH₃ CH₃ CH₃ (b) spinosyn C H CH₃

C₂H₅ CH₃ CH₃ CH₃ (c) spinosyn D CH₃ CH₃ (a) C₂H₅ CH₃ CH₃ CH₃ spinosyn E H CH₃ (a) CH₃ CH₃ CH₃ CH₃ spinosyn F H H (a) C₂H₅ CH₃ CH₃ CH₃ spinosyn G H CH₃

C₂H₅ CH₃ CH₃ CH₃ (d) spinosyn H H CH₃ (a) C₂H₅ H CH₃ CH₃ spinosyn J H CH₃ (a) C₂H₅ CH₃ H CH₃ spinosyn K H CH₃ (a) C₂H₅ CH₃ CH₃ H spinosyn L CH₃ CH₃ (a) C₂H₅ CH₃ H CH₃ spinosyn M H CH₃ (b) C₂H₅ CH₃ H CH₃ spinosyn N CH₃ CH₃ (b) C₂H₅ CH₃ H CH₃ spinosyn O CH₃ CH₃ (a) C₂H₅ CH₃ CH₃ H spinosyn P H CH₃ (a) C₂H₅ CH₃ H H spinosyn Q CH₃ CH₃ (a) C₂H₅ H CH₃ CH₃ spinosyn R H CH₃ (b) C₂H₅ H CH₃ CH₃ spinosyn S H CH₃ (a) CH₃ H CH₃ CH₃ spinosyn T H CH₃ (a) C₂H₅ H H CH₃ spinosyn U H CH₃ (a) C₂H₅ H CH₃ H spinosyn V CH₃ CH₃ (a) C₂H₅ H CH₃ H spinosyn W CH₃ CH₃ (a) C₂H₅ CH₃ H H spinosyn Y H CH₃ (a) CH₃ CH₃ CH₃ H spinosyn A 17- H CH₃ H C₂H₅ CH₃ CH₃ CH₃ Psa spinosyn D 17- CH₃ CH₃ H C₂H₅ CH₃ CH₃ CH₃ Psa spinosyn E 17- H CH₃ H CH₃ CH₃ CH₃ CH₃ Psa spinosyn F 17- H H H C₂H₅ CH₃ CH₃ CH₃ Psa spinosyn H 17- H CH₃ H C₂H₅ H CH₃ CH₃ Psa spinosyn J 17- H CH₃ H C₂H₅ CH₃ H CH₃ Psa spinosyn L 17- CH₃ CH₃ H C₂H₅ CH₃ H CH₃ Psa

TABLE 2

Factor R^(1′) R^(2′) R^(3′) R^(4′) R^(5′) spinosyn A9-Psa H CH₃

C₂H₅ H (a) spinosyn D9-Psa CH₃ CH₃ (a) C₂H₅ H spinosyn A H CH₃ H C₂H₅ H Aglycone spinosyn D CH₃ CH₃ H C₂H₅ H Aglycone

The naturally produced spinosyn compounds consist of a 5,6,5-tricylic ring system, fused to a 12-membered macrocyclic lactone, a neutral sugar (rhamnose) and an amino sugar (forosamine) (see Kirst et al. (1991). If the amino sugar is not present the compounds have been referred to as the pseudoaglycone of A, D, etc., and if the neutral sugar is not present then the compounds have been referred to as the reverse pseudoaglycone of A, D, etc. A more preferred nomenclature is to refer to the pseudoaglycones as spinosyn A 17-Psa, spinosyn D 17-Psa, etc., and to the reverse pseudoaglycones as spinosyn A 9-Psa, spinosyn D 9-Psa, etc.

The naturally produced spinosyn compounds may be produced via fermentation from cultures NRRL 18395, 18537, 18538, 18539, 18719, 18720, 18743 and 18823. These cultures have been deposited and made part of the stock culture collection of the Midwest Area Northern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, Ill. 61604.

U.S. Pat. No. 5,362,634 and corresponding European Patent Application No. 375316 A1 disclose spinosyns A, B, C, D, E, F, G, H, and J. These compounds are disclosed as being produced by culturing a strain of the novel microorganism Saccharopolyspora spinosa selected from NRRL 18395, NRRL 18537, NRRL 18538, and NRRL 18539.

WO 93/09126 disclosed spinosyns L, M, N, Q, R, S, and T. Also disclosed therein are two spinosyn J producing strains: NRRL 18719 and NRRL 18720, and a strain that produces spinosyns Q, R, S, and T: NRRL 18823.

WO 94/20518 and U.S. Pat. No. 5,6704,486 disclose spinosyns K, O, P, U, V, W, and Y, and derivatives thereof. Also disclosed is spinosyn K-producing strain NRRL 18743.

A challenge in producing spinosyn compounds arises from the fact that a very large fermentation volume is required to produce a very small quantity of spinosyns. It is highly desired to increase spinosyn production efficiency and thereby increase availability of the spinosyns while reducing their cost. A cloned fragment of DNA containing genes for spinosyn biosynthetic enzymes would enable duplication of genes coding for rate limiting enzymes in the production of spinosyns. This could be used to increase yield in any circumstance when one of the encoded activities limited synthesis of the desired spinosyn. A yield increase of this type was achieved in fermentations of Streptomyces fradiae by duplicating the gene encoding a rate-limiting methyltransferase that converts macrocin to tylosin (Baltz et al., 1997).

Cloned biosynthetic genes would also provide a method for producing new derivatives of the spinosyns which may have a different spectrum of insecticidal activity. New derivatives are desirable because, although known spinosyns inhibit a broad spectrum of insects, they do not control all pests. Different patterns of control may be provided by biosynthetic intermediates of the spinosyns, or by their derivatives produced in vivo, or by derivatives resulting from their chemical modification in vitro. Specific intermediates (or their natural derivatives) could be synthesized by mutant strains of S. spinosa in which certain genes encoding enzymes for spinosyn biosynthesis have been disrupted. Such strains can be generated by integrating, via homologous recombination, a mutagenic plasmid containing an internal fragment of the target gene. Upon plasmid integration, two incomplete copies of the biosynthetic gene are formed, thereby eliminating the enzymatic function it encoded. The substrate for this enzyme, or some natural derivative thereof, should accumulate upon fermentation of the mutant strain. Such a strategy was used effectively to generate a strain of Saccharopolyspora erythraea producing novel 6-deoxyerythromycin derivatives (Weber & McAlpine, 1992).

Novel intermediates could also be synthesized by mutant strains of S. spinosa in which parts of certain genes encoding enzymes for spinosyn biosynthesis have been replaced with parts of the same gene which have been specifically mutated in vitro, or with corresponding parts of genes from other organisms. Such strains could be generated by swapping the target region, via double homologous recombination, with a mutagenic plasmid containing the new fragment between non-mutated sequences which flank the target region. The hybrid gene would produce protein with altered functions, either lacking an activity or performing a novel enzymatic transformation. A new derivative would accumulate upon fermentation of the mutant strain. Such a strategy was used to generate a strain of Saccharopolyspora erythraea producing a novel anhydroerythromycin derivative (Donadio et al., 1993).

Biosynthesis of spinosyns proceeds via stepwise condensation and modification of 2- and 3-carbon carboxylic acid precursors, generating a linear polyketide that is cyclized and bridged to produce the tetracyclic aglycone. Pseudoaglycone (containing tri-O-methylated rhamnose) is formed next, then di-N-methylated forosamine is added to complete the biosynthesis (Broughton et al., 1991). Other macrolides, such as the antibiotic erythromycin, the antiparasitic avermectin and the immunosuppressant rapamycin, are synthesized in a similar fashion. In the bacteria producing these compounds, most of the macrolide biosynthetic genes are clustered together in a 70–80 kb region of the genome (Donadio et al., 1991). At the centers of these clusters are 3–5 highly conserved genes coding for the very large, multifunctional proteins of a Type I polyketide synthase (PKS). Together the polypeptides form a complex consisting of an initiator module and several extender modules, each of which adds a specific acyl-CoA precursor to a growing polyketide chain, and modifies the β-keto group in a specific manner. The structure of a polyketide is therefore determined by the composition and order of the modules in the PKS. A module comprises several domains, each of which performs a specific function. The initiator module consists of an acyl transferase (AT) domain for addition of the acyl group from the precursor to an acyl carrier protein (ACP) domain. The extender modules contain these domains, along with a β-ketosynthase (KS) domain that adds the pre-existing polyketide chain to the new acyl-ACP by decarboxylative condensation. Additional domains may also be present in the extender modules to carry out specific β-keto modifications: a β-ketoreductase (KR) domain to reduce the β-keto group to a hydroxyl group, a dehydratase (DH) domain to remove the hydroxyl group and leave a double bond, and an enoyl reductase (ER) domain to reduce the double bond and leave a saturated carbon. The last extender module terminates with a thioesterase (TE) domain that liberates the polyketide from the PKS enzyme in the form of a macrocyclic lactone.

Macrolides are derived from macrocyclic lactones by additional modifications, such as methylation and changes in reductive state, and the addition of unusual sugars. Most of the genes required for these modifications, and for the synthesis and attachment of the sugars, are clustered around the PKS genes. The genes encoding deoxysugar biosynthetic enzymes are similar in producers of macrolide antibiotics, such as erythromycin and tylosin (Donadio et al., 1993), and producers of extracellular polysaccharides, such as the O-antigens of Salmonella and Yersinia (Jiang et al., 1991). All these syntheses involve activation of glucose by the addition of a nucleotide diphosphate, followed by dehydration, reduction and/or epimerization. The resultant sugar could undergo one or more modifications such as deoxygenation, transamination and methylation, depending upon the type of sugar moiety present in the macrolide. The sugars are incorporated into macrolides by the action of specific glycosyltransferases. Genes involved in the synthesis and attachment of a sugar may be tightly clustered—even transcribed as a single operon—or they may be dispersed. Spinosyn synthesis also involves bridging of the lactone nucleus, an activity that is rare in macrolide producers. Therefore, the spinosyn biosynthetic cluster may uniquely contain additional genes encoding enzymes for this function.

The following terms are used herein as defined below:

AmR—the apramycin resistance-conferring gene.

ApR—the ampicillin resistance-conferring gene.

ACP—acyl carrier protein.

AT—acyltransferase.

bp—base pairs.

Cloning—the process of incorporating a segment of DNA into a recombinant DNA cloning vector and transforming a host cell with the recombinant DNA.

CmR—the chloramphenicol resistance-conferring gene.

Codon bias—the propensity to use a particular codon to specify a specific amino acid. In the case of S. spinosa, the propensity is to use a codon having cytosine or guanine as the third base.

Complementation—the restoration of a mutant strain to its normal phenotype by a cloned gene.

Conjugation—a process in which genetic material is transferred from one bacterial cell to another.

cos—the lambda cohesive end sequence.

Cosmid—a recombinant DNA cloning vector which is a plasmid that not only can replicate in a host cell in the same manner as a plasmid but also can be packaged into phage heads.

DH—dehydratase.

ER—enoyl reductase.

Exconjugant—recombinant strain derived from a conjugal mating.

Gene—a DNA sequence that encodes a polypeptide.

Genomic Library—a set of recombinant DNA cloning vectors into which segments of DNA, representing substantially all DNA sequences in a particular organism have been cloned.

Homology—degree of similarity between sequences

Hybridization—the process of annealing two single stranded DNA molecules to form a double stranded DNA molecule, which may or may not be completely base paired.

In vitro packaging—the in vitro encapsulation of DNA in coat protein to produce a virus-like particle that can introduce DNA into a host cell by infection

kb—kilo base pairs.

KR—β-keto reductase.

KS—ketosynthase.

Mutagenesis—creation of changes in DNA sequence. They can be random or targeted, generated in vivo or in vitro. Mutations can be silent, or can result in changes in the amino acid sequence of the translation product which alter the properties of the protein and produce a mutant phenotype.

NmR—the neomycin resistance-conferring gene.

ORF—open reading frame.

ori—a plasmid origin of replication (oriR) or transfer (oriT).

PKS—polyketide synthase.

Promoter—a DNA sequence that directs the initiation of transcription.

Recombinant DNA cloning vector—any autonomously replicating or integrating agent, including, but not limited to, plasmids, comprising a DNA molecule to which one or more additional DNA molecules can be or have been added.

Recombinant DNA methodology—technologies used for the creation, characterization, and modification of DNA segments cloned in recombinant DNA vectors.

Restriction fragment—any linear DNA molecule generated by the action of one or more restriction enzymes.

Spinosyn—a fermentation product typically characterized by a 5,6,5-tricylic ring system, fused to a 12-membered macrocyclic lactone, a neutral sugar (rhamnose) and an amino sugar (forosamine), or a similar macrocyclic lactone fermentation product produced by a microorganism utilizing all or most of the spinosyn genes.

Spinosyn genes—the DNA sequences that encode the products required for spinosyn biosynthesis, more specifically the genes spnA, spnB, spnC, spnD, spnE, spnF, spnG, spnH, spnI, spnJ, spnK, spnL, spnM, spnN, spnO, spnP, spnQ, spnR, spnS, S. spinosa gtt, S. spinosa gdh, S. spinosa epi, and S. spinosa kre, as described hereinafter, or functional equivalents thereof.

Subclone—a cloning vector with an insert DNA derived from another DNA of equal size or larger.

TE—thioesterase.

Transformation—the introduction of DNA (heterologous or homologous) into a recipient host cell that changes the genotype and results in a change in the recipient cell.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a diagram illustrating the spinosyn biosynthetic pathway.

FIG. 2 is a map illustrating the arrangement of BamHI fragments and open reading frames in the cloned region of S. spinosa DNA.

FIG. 3 is a restriction site and functional map of Cosmid pOJ436.

FIG. 4 is a restriction site and functional map of Cosmid pOJ260.

FIG. 5 is a restriction site and functional map of pDAB1523.

BRIEF DESCRIPTIONS OF THE INVENTION

Spinosyn biosynthetic genes and related ORFs were cloned and the DNA sequence of each was determined. The cloned genes and ORFs are designated hereinafter as spnA, spnB, spnC, spnD, spnE, spnF, spnG, spnH, spnI, spnJ, spnK, spnL, spnM, spnN, spnO, spnP, spnQ, spnR, spnS, ORFL15, ORFL16, ORFR1, ORFR2, S. spinosa gtt, S. spinosa gdh, S. spinosa epi, and S. spinosa kre. The proposed functions of the cloned genes in spinosyn biosynthesis are identified FIG. 1 and in the discussion hereinafter.

In one of its aspects, the invention provides an isolated DNA molecule comprising a DNA sequence that encodes a spinosyn biosynthetic enzyme, wherein said enzyme is defined by an amino acid sequence selected from the group consisting of SEQ ID NOS 2–5, 7–24, 26, 27, 29, and 33, or said enzyme is defined by one of said amino acid sequences in which one or more amino acid substitutions have been made that do not affect the functional properties of the encoded enzyme. In a preferred embodiment, the DNA sequence is selected from the group of genes consisting of spnA, spnB, spnC, spnD, spnE, spnF, spnG, spnH, spnI, spnJ, spnK, spnL, spnM, spnN, spnO, spnP, spnQ, spnR, spnS, ORFL15, ORFL16, ORFR1, ORFR2, S. spinosa gtt, S. spinosa gdh, S. spinosa epi, and S. spinosa kre, said genes being described by, respectively, bases 21111–28898, 28916–35374, 35419–44931, 44966–59752, 59803–76569, 20168–20995, 18541–19713, 17749–18501, 16556–17743, 14799–16418, 13592–14785, 12696–13547, 11530–12492, 10436–11434, 8967–10427, 7083–8450, 5363–6751, 4168–5325, 3416–4165, 2024–2791, 1135–1971, 76932–77528 and 77729–79984 of SEQ ID NO:1, bases 334–1119 of SEQ ID NO:27, bases 88–1077 of SEQ ID NO 25, bases 226–834 of SEQ ID NO 32, and bases 1165–1992 of SEQ ID NO:25.

In another of its aspects, the invention provides an isolated DNA molecule comprising a DNA sequence that encodes a spinosyn PKS domain selected from KSi, ATi, ACPi, KS1, AT1, KR1, and ACP1, said domains being described by, respectively, amino acids 6–423, 528–853, 895–977, 998–1413, 1525–1858, 2158–2337, and 2432–2513 of SEQ ID NO:2. In a preferred embodiment, the DNA sequence is selected from the group consisting of bases 21126–22379, 22692–23669, 23793–24041, 24102–25349, 25683–26684, 27582–28121, and 28404–28649 of SEQ ID NO:1.

In another of its aspects, the invention provides an isolated DNA molecule comprising a DNA sequence that encodes a spinosyn PKS domain selected from KS2, AT2, DH2, ER2, KR2, and ACP2, said domains being described by, respectively, amino acids 1–424, 536–866, 892–1077, 1338–1683, 1687–1866, and 1955–2034 of SEQ ID NO:3. In a preferred embodiment the DNA sequence is selected from the group consisting of bases 29024–30295, 30629–31621, 31697–32254, 33035–34072, 34082–34621, 34886–35125 of SEQ ID NO:1.

In another of its aspects, the invention provides an isolated DNA molecule comprising a DNA sequence that encodes a spinosyn PKS domain selected from KS3, AT3, KR3, ACP3, KS4, AT4, KR4, and ACP4, said domains being described by, respectively, amino acids 1–423, 531–280, 1159–1337, 1425–1506, 1529–1952, 2066–2396, 2700–2880, and 2972–3053 of SEQ ID NO:4. In a preferred embodiment the DNA sequence is selected from the group consisting of bases 35518–36786, 37108–38097, 38992–39528, 39790–40035, 40102–41373, 41713–42705, 43615–44157, and 44431–44676 of SEQ ID NO:1.

In another of its aspects the invention provides an isolated DNA molecule comprising a DNA sequence that encodes a spinosyn PKS domain selected from KS5, AT5, DH5, KR5, ACP5, KS6, AT6, KR6, ACP6, KS7, AT7, KR7, and ACP7, said domains being described by, respectively, amino acids 1–424, 539–866, 893–1078, 1384–1565, 1645–1726, 1748–2172, 2283–2613, 2916–3095, 3188–3269, 3291–3713, 3825–4153, 4344–4638, and 4725–4806 of SEQ ID NO:5. In a preferred embodiment the DNA sequence is selected from the group consisting of bases 45077–46348, 46691–47674, 47753–48310, 49226–49771, 50009–50254, 50318–51592, 51923–52915, 53822–54361, 54638–54883, 54947–56215, 56549–57535, 58106–58990, and 59249–59494 of SEQ ID NO:1.

In another of its aspects, the invention provides an isolated DNA molecule comprising a DNA sequence that encodes a spinosyn PKS domain selected from KS8, AT8, DH8, KR8, ACP8, KS9, AT9, DH9, KR9, ACP9, KS10, AT10, DH10, KR10, ACP 10, and TE10, said domains being described by, respectively, amino acids 1–424, 530–848, 883–1070, 1369–1552, 1648–1726, 1749–2173, 2287–2614, 2640–2800, 3157–3341, 3422–3500, 3534–3948, 4060–4390, 4413–4597, 4900–5078, 5172–5253, and 5302–5555 of SEQ ID NO:6. In a preferred embodiment, the DNA sequence is selected from the group consisting of bases 59902–61173, 61489–62445, 62548–63111, 64006–64557, 64843–65079, 65146–66420, 66760–67743, 67819–68301, 69370–69924, 70165–70401, 70471–71745, 72079–73071, 73138–73692, 74599–75135, 75415–75660, and 75805–76566 of SEQ ID NO:1.

In another of its aspects the invention provides an isolated DNA molecule comprising a DNA sequence that encodes a spinosyn PKS module, said module being selected from the group consisting of amino acids 6–1413 of SEQ ID NO:2, 1525–2513 of SEQ ID NO:2, 1–2034 of SEQ ID NO:3, 1–1506 of SEQ ID NO:4, 1529–3053 of SEQ ID NO:4, 1–1726 of SEQ ID NO:5, 1748–3269 of SEQ ID NO:5, 3291–4806 of SEQ ID NO:5, 1–1726 of SEQ ID NO:5, 1–1726 of SEQ ID NO:6, 1749–3500 of SEQ ID NO:6, and 35434–5555 of SEQ ID NO:6. In a preferred embodiment the DNA sequence is selected from the group consisting of bases 21126–24041, 24102–28649, 29024–35125, 35518–40035, 40102–44676, 45077–50254, 50318–54883, 54947–59494, 59902–65079, 65146–70401, and 70471–76566 of SEQ ID NO:1.

In another of its aspects, the invention provides a recombinant DNA vector which comprises a DNA sequence of the invention as described above.

In another of its aspects the invention provides a host cell transformed with a recombinant vector of the invention as described above.

In another of its aspects, the invention provides a method of increasing the spinosyn-producing ability of a spinosyn-producing microorganism comprising the steps of

1) transforming with a recombinant DNA vector or portion thereof a microorganism that produces spinosyn or a spinosyn precursor by means of a biosynthetic pathway, said vector or portion thereof comprising a DNA sequence of the invention, as described above, that codes for the expression of an activity that is rate limiting in said pathway, and

2) culturing said microorganism transformed with said vector under conditions suitable for cell growth and division, expression of said DNA sequence, and production of spinosyn.

In another of its aspects the invention provides a spinosyn-producing microorganism having operative spinosyn biosynthetic genes wherein at least one of the spinosyn biosynthetic genes spnA, spnB, spnC, spnD, spnE, spnF, spnG, spnH, spnI, spnJ, spnK, spnL, spnM, spnN, spnO, spnP, spnQ, spnR, spnS, S. spinosa gtt, S. spinosa gdh, S. spinosa epi, or S. spinosa kre has been duplicated.

In another of its aspects the invention provides a spinosyn-producing microorganism, said microorganism having spinosyn biosynthetic genes in its genome, wherein at least one of said genes has been disrupted by recombination with an internal fragment of that gene, the rest of said genes being operational to produce a spinosyn other than the one that would be produced if the disrupted gene were operational. Preferably the microorganism is an S. spinosa mutant.

The invention also provides a spinosyn-producing microorganism having operational spinosyn biosynthetic genes in its genome, wherein said genes a) include at least one operational PKS module more than or at least one less than is present in SEQ ID NO:1; or b) include a PKS module that differs from the corresponding module described in SEQ ID NO:1 by the deletion, inactivation, or addition of a KR, DH or ER domain, or by the substitution of an AT domain. Preferably the microorganism is an S. spinosa mutant.

The invention also provides spinosyns produced by cultivation of the novel microorganisms of the invention.

In another of its aspects the invention provides a process for isolating spinosyn biosynthetic genes which comprises creating a genomic library of a spinosyn producing microorganism, and using a labeled fragment of SEQ ID NO:1 that is at least 20 bases long as a hybridization probe.

DETAILED DESCRIPTION OF THE INVENTION

A cosmid library of S. spinosa (NRRL 18395) DNA was constructed from fragments generated by partial digestion with Sau3A I. They were cloned into the BamHI site of vector pOJ436 (See FIG. 3) (Bierman et al., 1992) and introduced into E. coli cells by in vitro packaging and transduction. The library of recombinant bacteria thus prepared was screened for homology to two radiolabelled DNA probes by hybridization using the methods of Solenberg & Burgett (1989). One probe was the 400 kb SpeI fragment which is often deleted in non-producing S. spinosa strains generated by transformation or mutagenesis with N-methyl-N′-nitro-N-nitrosoguanidine (Matsushima et al., 1994). The second probe was a 300 bp piece of S. spinosa DNA that codes for part of a ketosynthase not involved in spinosyn biosynthesis (B. E. Schoner, personal communication). It includes a region which is highly conserved in all polyketide and fatty acid synthase genes, and was therefore expected to cross-hybridize with the spinosyn PKS genes. Cosmids 9A6 and 2C10 were two of seven clones that hybridized to both probes. Cosmid 3E11 was selected from the genomic library by hybridization to a radiolabelled SgrA1-BamH1 fragment of cosmid 9A6 (bases 26757–26936 in SEQ ID NO: 1). To determine the nucleotide sequence of the insert in cosmid 9A6, BamHI fragments were subcloned into the BamHI site of plasmid pOJ260 (See FIG. 4) (Bierman et al., 1992). The sequences of the inserts in these plasmids were determined by either of two methods. In one method, subcloned fragments were partially digested with Sau3A I, and size-selected pieces were cloned into the BamHI site of DNA from the phage M13 mp19. Single-stranded DNA was prepared from randomly selected recombinants, and sequenced by fluorescent cycle sequencing using reagents and equipment from ABI (Applied Biosystems, Inc., Foster, Calif.), according to the methods of Burgett & Rosteck (1994). The sequences from phage subclones of each plasmid were assembled into one contiguous sequence. In the other sequencing method, double-stranded plasmid DNAs were primed reiteratively with single-stranded oligonucleotides, each designed to complement a region near the end of previously determined sequence. The complete sequence was thus compiled from a series of partially-overlapping sequences. Prism-Ready Sequencing Kits (ABI) were used according to the manufacturer's instructions, and analyzed on an ABI373A Sequencer. The same strategy was employed to sequence across the BamHI sites of double-stranded 9A6 DNA. These data allowed the subcloned sequences to be aligned and oriented relative to one another using the AssemblyLIGN module of the MacVector program (Oxford Molecular, Campbell, Ky.), and thereby allowed the entire nucleotide sequence of the S. spinosa DNA in cosmid 9A6 to be assembled. The complete sequences of cosmids 2C10 and 3E11 were determined by the method of fluorescent cycle sequencing of random DNA fragments cloned in phage M13 (SeqWright, Houston, Tex.). The inserts in cosmids 2C10 and 3E11 overlapped, and the insert in 3E11 overlapped the end of the insert in cosmid 9A6. See FIG. 2. Together, the three cosmid inserts spanned about 80 kb of unique sequence (SEQ ID NO: 1). The following Table 3 identifies the portions of SEQ ID NO:1 included in each of the three inserts.

TABLE 3 insert bases in SEQ ID NO:1 cosmid 9A6   1–26941 cosmid 3E11 23489–57287 cosmid 2C10 (corrected) 41429–80161 FIG. 2 gives a graphical representation of the relationship of the three inserts to the 80 kb of sequence.

It should be noted that cosmid 2C10 was missing bases G41877, C45570, C57845 and G73173 of SEQ ID NO:1. These deletions were determined to be cloning artifacts. The deletions generated in-frame stop codons that truncated PKS polypeptides. One of them occurred in a region also cloned in cosmid 3E11, but was not present in the region of 3E11 for which sequence was obtained. Uncloned DNA spanning all 8 stop codons in the PKS region was therefore sequenced directly from PCR-amplified regions of the genome of S. spinosa (NRRL 18395). The sequences from uncloned DNA confirmed the existence of the 4 stop codons at the end of ACP domains, and proved that the 4 frameshifts within other coding regions were cloning artifacts unique to cosmid 2C10.

PKS Genes

SEQ ID NO:1 includes a central region of about 55 kb with striking homology to the DNA encoding the polyketide synthases of known macrolide producers (Donadio et al., 1991; Dehoff et al., 1997). The spinosyn PKS DNA region consists of 5 ORFs with in-frame stop codons at the end of ACP domains, similar to the PKS ORFs in the other macrolide-producing bacteria. The five spinosyn PKS genes are arranged head-to-tail (see FIG. 2), without any intervening non-PKS functions such as the insertion element found between the erythromycin PKS genes AI and AII (Donadio et al., 1993). They are designated spnA, spnB, spnC, spnD, and spnE. The nucleotide sequence for each of the five spinosyn PKS genes, and the corresponding polypeptides, are identified in the following Table 4:

TABLE 4 CORRESPONDING GENE BASES IN SEQ ID NO:1 POLYPEPTIDE spnA 21111–28898 SEQ ID NO:2 spnB 28916–35374 SEQ ID NO:3 spnC 35419–44931 SEQ ID NO:4 spnD 44966–59752 SEQ ID NO:5 spnE 59803–76569 SEQ ID NO:6

spnA encodes the initiator module (SEQ ID NO:1, bases 21126–24041) and extender module 1 (SEQ ID NO:1, bases 24102–28649). The nucleotide sequence and corresponding amino acid sequence for each of the functional domains within the initiator module and extender module 1 are identified in the following Table 5:

TABLE 5 spnA AMINO DOMAIN BASES IN SEQ ID NO:1 ACIDS IN SEQ ID NO:2 KSi 21126–22379  6–423 ATi 22692–23669 528–853 ACPi 23793–24041 895–977 KS1 24102–25349  998–1413 AT1 25683–26684 1525–1858 KR1 27582–28121 2158–2337 ACP1 28404–28649 2432–2513

spnB encodes extender module 2 (SEQ ID NO:1, bases 29024–35125). The nucleotide sequence and corresponding amino acid sequence for each of the functional domains within extender module 2 are identified in the following Table 6:

TABLE 6 spnB AMINO ACIDS DOMAIN BASES IN SEQ ID NO:1 IN SEQUENCE ID NO.3 KS2 29024–30295  1–424 AT2 30629–31621 536–866 DH2 31697–32254  892–1077 ER2 33035–34072 1338–1683 KR2 34082–34621 1687–1866 ACP2 34886–35125 1955–2034

spnC encodes extender module 3 (SEQ ID NO:1, bases 35518–40035) and extender module 4 (SEQ ID NO:1, bases 40102–44676). The nucleotide sequence and corresponding amino acid sequence for each of the functional domains within extender modules 3 and 4 are identified in the following Table 7:

TABLE 7 spnC AMINO DOMAIN BASES IN SEQ ID NO:1 ACIDS IN SEQ ID NO:4 KS3 35518–36786  1–423 AT3 37108–38097 531–280 KR3 38992–39528 1159–1337 ACP3 39790–40035 1425–1506 KS4 40102–41373 1529–1952 AT4 41713–42705 2066–2396 KR4 43615–44157 2700–2880 ACP4 44431–44676 2972–3053

spnD encodes extender module 5 (SEQ ID NO:1, bases 45077–50254), extender module 6 (SEQ ID NO:1, bases 50318–54883), and extender module 7 (SEQ ID NO:1, bases 54947–59494). The nucleotide sequence and corresponding amino acid sequence for each of the functional domains within extender modules 5, 6, and 7 is identified in the following Table 8:

TABLE 8 spnD AMINO DOMAIN BASES IN SEQ ID NO:1 ACIDS IN SEQ ID NO:5 KS5 45077–46348  1–424 AT5 46691–47674 539–866 DH5 47753–48310  893–1078 KR5 49226–49771 1384–1565 ACP5 50009–50254 1645–1726 KS6 50318–51592 1748–2172 AT6 51923–52915 2283–2613 KR6 53822–54361 2916–3095 ACP6 54638–54883 3188–3269 KS7 54947–56215 3291–3713 AT7 56549–57535 3825–4153 KR7 58106–58990 4344–4638 ACP7 59249–59494 4725–4806

spnE encodes extender module 8 (SEQ ID NO:1, bases 59902–65079), extender module 9 (SEQ ID NO:1, bases 65146–70401), and extender module 10 (SEQ ID NO:1, bases 70471–76566). The nucleotide sequence and corresponding amino acid sequence for each of the functional domains within extender modules 8, 9, and 10 is identified in the following Table 9:

TABLE 9 spnE AMINO DOMAIN BASES IN SEQ ID NO:1 ACIDS IN SEQ ID NO:6 KS8 59902–61173  1–424 AT8 61489–62445 530–848 DH8 62548–63111  883–1070 KR8 64006–64557 1369–1552 ACP8 64843–65079 1648–1726 KS9 65146–66420 1749–2173 AT9 66760–67743 2287–2614 DH9 67819–68301 2640–2800 KR9 69370–69924 3157–3341 ACP9 70165–70401 3422–3500 KS10 70471–71745 3534–3948 AT10 72079–73071 4060–4390 DH10 73138–73692 4413–4597 KR10 74599–75135 4900–5078 ACP10 75415–75660 5172–5253 TE10 75805–76566 5302–5555

The boundaries and functions of the 50 domains identified in the foregoing Tables 5–9 are predicted based on similarities to the conserved amino acid sequences of the domains in other polyketide synthases, particularly the erythromycin polyketide synthase (Donadio et al., 1992). The unexpected KSi domain at the amino terminus of the initiator module is presumed to be non-functional because it contains a glutamine residue at amino acid 172, in place of the cysteine required for β-ketosynthase activity (Siggard-Andersen, 1993). A similar non-functional KS domain has been discovered in the initiator module of the tylosin PKS (Dehoff et al., 1997). The other spinosyn PKS domains are functional. None of them has the sequence characteristics of the inactive domains found in the erythromycin and rapamycin PKS genes (Donadio et al., 1991; Aparicio et al., 1996). The cloned PKS genes were shown to be essential for spinosyn biosynthesis by the discovery that strains of S. spinosa in which these genes had been disrupted were unable to produce spinosyns by fermentation. Gene disruption was achieved by cloning an internal fragment of the gene into plasmid pOJ260 (FIG. 4), using procedures well-known to those skilled in the art. The recombinant plasmids were then introduced into S. spinosa by conjugation from E. coli using the procedures of Matsushima et al. (1994), and selecting for apramycin-resistant exconjugants. Plasmids based on pOJ260 do not replicate independently in S. spinosa, and are stably maintained by integrating the plasmid into the chromosome via recombination between the cloned DNA and its homologous sequence in the genome. Integration creates two incomplete versions of the targeted gene (one lacking 5′ sequences and one lacking 3′ sequences) in the chromosome, with the pOJ260 DNA between them. Spinosyn biosynthesis was blocked by disrupting the spnA ORF with the BamH1 fragments V, N, or K, corresponding respectively to the following segments of SEQ ID NO: 1: 21365–22052, 22052–24338, or 24338–26227. Spinosyn biosynthesis was also blocked by disrupting the spnD ORF with BamH1 fragments G, E, or K, corresponding respectively to the following segments of SEQ ID NO: 1: bases 48848–50578, 50578–52467, or 55207–55888. Spinosyn biosynthesis was also blocked by disrupting the spnE ORF with BamH1 fragments J, I, D, H, and F, corresponding respectively to the following segments of SEQ ID NO: 1: 63219–63989, 65406–66733, 66733–68997, 69369–70731, and 70731–72675. Spinosyn biosynthesis was not blocked by integration via BamH1 fragments C (bases 44612–47565 in SEQ ID NO: 1) or B (bases 55936–63219 in SEQ ID NO: 1) because they are not internal to any one gene; BamH1 fragment C spans the junction between spnC and spnD, and BamH1 fragment B spans the junction between spnD and spnE. In these cases, integration leaves one complete version of each gene.

Genes Adjacent to the PKS Responsible for Additional Modifications

In the DNA upstream of the PKS genes (cloned in cosmid 9A6) there were 16 open reading frames (ORFs), each consisting of at least 100 codons, beginning with ATG or GTG and ending with TAA, TAG or TGA, and having the codon bias expected of protein-coding regions in an organism whose DNA contains a high percentage of guanine and cytosine residues (Bibb et al, 1984). See the bottom right hand side of FIG. 2 for a graphical representation of the 16 ORFs in 9A6. Based on evidence that will be discussed hereinafter, 14 of the ORFs have been designated as spinosyn biosynthetic genes, namely: spnF, spnG, spnH, spnI, spnJ, spnK, spnL, spnM, spnN, spnO, spnP, spnQ, spnR, and spnS (they are labeled F through S in FIG. 2). In the following Table 10, the DNA sequence and the amino acid sequence for the corresponding polypeptide are identified for each of these genes, as well as for two ORFs (ORFL15 and ORFL16) found immediately upstream of spnS. Also identified in Table 10 are the nucleotide sequences for ORFR1 and ORFR2 downstream of the PKS genes (in cosmid 2C10), and the amino acid sequences corresponding to them.

TABLE 10 GENE BASES IN SEQUENCE ID NO: 1 POLYPEPTIDE spnF 20168–20995 SEQ ID NO: 7  spnG 18541–19713 (C) SEQ ID NO: 8  spnH 17749–18501 (C) SEQ ID NO: 9  spnI 16556–17743 SEQ ID NO: 10 spnJ 14799–16418 (C) SEQ ID NO: 11 spnK 13592–14785 (C) SEQ ID NO: 12 spnL 12696–13547 (C) SEQ ID NO: 13 spnM 11530–12492 (C) SEQ ID NO: 14 spnN 10436–11434 SEQ ID NO: 15 spnO 8967–10427 SEQ ID NO: 16 spnP 7083–8450  SEQ ID NO: 17 spnQ 5363–6751  (C) SEQ ID NO: 18 spnR 4168–5325  (C) SEQ ID NO: 19 spnS 3416–4165  (C) SEQ ID NO: 20 ORFL 15 2024–2791  SEQ ID NO: 21 ORFL 16 1135–1971  (C) SEQ ID NO: 22 ORFR 1 76932–77528 SEQ ID NO: 23 ORFR 2 77729–79984 SEQ ID NO: 24 (C) indicates complementary strand is given in the sequence listing

To assign functions to the polypeptides identified in Table 10, three lines of evidence were utilized: similarity to sequences of known function, results of targeted gene disruption experiments, and results of bioconversion experiments.

The amino acid sequences of the predicted polypeptides were compared to sequences deposited in the databases at the National Center for Biotechnology Information (NCBI, Washington, D.C.), using the BLAST algorithm to determine how well they are related to known proteins. The BLAST searches of the NCBI databases were also repeated periodically to obtain new insights from additional homologies. Table 11 gives the best matches from a basic BLAST search on Jan. 12, 1998:

TABLE 11 Significant GenBank BLAST Reported Gene Protein Match Accession Score* function spnF C-24 sterol methyl- U79669 202 C-methylation transferase (Zea mays) spnG Daunosamyl trans- L47164 202 sugar addition ferase dnrS (Streptomyces peucetius) spnH Mycinamicin III O- D16097 408 sugar methyltransferase methylation (Micromonospora griseorubida) spnI ORFY (Streptomyces Z48262 192 unknown nogalater) spnJ Hexose oxidase U89770 143 oxido- (Chondrus crispus) reduction spnK ORFY (Streptomyces Z48262 137 unknown nogalater) spnL C-24 sterol methyl- U79669 166 C-methylation transferase (Zea mays) spnM Unknown Z95586 132 unknown (Mycobacterium tuberculosis) spnN RdmF (Streptomyces U10405 409 unknown purpurascens) spnO 2,3 dehydratase Y11199 595 deoxysugar EryBV1 synthesis (Saccharopolyspora erythraea) spnP Mycarosyl transferase U77459 336 sugar addition EryBV (Saccharopolyspora erythraea) spnQ CDP-4-keto-6-deoxy- P26398 784 dideoxysugar D-glucose-3-dehydrase synthesis (Salmonella enterica) spnR Spore coat P39623 286 sugar polysaccharide transamination biosynthesis protein (Bacillus subtilis) spnS TDP-N- U77459 484 aminosugar dimethyldesosamine- methylation N-methyltransferase EryCVI (Saccharopolyspora erythraea) ORFL15 Keto acyl reductase Z11511 132 oxido- (Streptomyces reduction cinnamonensis) ORFL16 Regulatory protein of transcription the als operon, control (Bacillus subtilis) ORFR1 None ORFR2 Conjugation transfer Z99117 328 DNA protein replication (Bacillus subtilis) *Greater similarity is associated with higher BLAST scores (Altschul et al., 1990).

In targeted gene disruptions, internal fragments were generated by PCR amplification from the cosmid DNAs, and cloned into plasmid pOJ260. The resulting plasmids were then conjugated into S. spinosa (NRRL 18395), and apramycin-resistant exconjugants were isolated and fermented. As stated earlier, the basis of disruption experiments is that when a plasmid bearing an internal gene fragment is integrated, two incomplete copies of the biosynthetic gene result, thereby eliminating the enzymatic function. Resulting fermentation products were analyzed to determine which spinosyns accumulated. The results of the targeted gene disruption experiments are summarized in Table 12.

In bioconversion studies, strains in which spinosyn synthesis was altered were tested for their ability to convert available spinosyn intermediates to other spinosyns. The intermediates used were spinosyn A Aglycone (AGL), spinosyn P(P), spinosyn K (K), and spinosyn A 9-Psa (PSA). The results of the bioconversion experiments are also summarized in Table 12

TABLE 12 Internal Fragment in spinosyns Disrupted SEQ ID NO: accumu- Bioconversion products Gene 1 lated AGL→ P→ K→ PSA→ None None A + D spnF 20325–20924 None A A A spnG 18818–19426 None AGL K A spnG–H 18511–19559 P K A spnI 16699–17400 None J A A spnJ 14866–15470 None A A spnK 13785–14574 None spnL 12791–13428 None A A A spnM 11705–12371 3% A A A spnN 10636–11369 PSA spnO  9262–10226 PSA spnP 7391–8159 PSA PSA ORFL15 2145–2719 A + D ORFL16 1226–1852 A + D ORFR2 79321–79855 A + D

The conclusions drawn from BLAST searches, the gene disruption experiments, and the bioconversion studies will now be discussed in greater detail on a gene by gene basis.

The 11 genes upstream of the PKS were shown to be involved in spinosyn biosynthesis because strains in which they were disrupted failed to accumulate the major spinosyns A and D (Table 12). The next 2 genes upstream (ORFL15, ORFL16), and the large gene downstream (ORFR2) of the PKS, do not contribute to spinosyn production because fermentation was not affected by their disruption (Table 12). Disruption of the ORF immediately downstream of the PKS genes (ORFR1) was not attempted because it was too small to yield an internal fragment that would recombine at an acceptable frequency. Disruptions of the spnQ, spnR, and spnS genes were not attempted because early BLAST searches showed that these genes had striking similarity to enzymes known to be involved in the biosynthesis of unusual deoxysugars. spnQ had 53% identity between its gene product and the CDP-4-keto-6-deoxy-D-glucose-3-dehydrase involved in synthesis of the abequose moiety of the Salmonella enterica cell surface lipopolysaccharide (Jiang et al., 1991); spnR had up to 40% identity between its product and a group of proteins proposed to function as deoxysugar transaminases (Thorson et al., 1993); and spnS had 42% identity between its product and the SrmX product of Streptomyces ambofaciens, an organism that synthesizes the forosamine-containing antibiotic spiramycin (Geistlich et al., 1992). Even stronger similarities have emerged from recent BLAST searches (Table 11). Based on these similarities, and the close linkage of the genes to other spinosyn biosynthetic genes, it is concluded that spnQ spnR, and spnS are involved in production of the forosamine moiety of spinosyns.

spnF, spnJ, spnL, spnM

Strains disrupted in genes spnF, spnJ, spnL or spnM did not accumulate any spinosyns to significant levels (the low level of spinosyn A in the spnM mutant presumably resulted from some residual activity in the gene product deleted at its carboxy terminus). However, they bioconverted exogenously-supplied aglycone to spinosyn A, and therefore contained all the enzymes necessary for the later steps in spinosyn biosynthesis. These particular genes must be involved in generation of the aglycone from the putative monocyclic lactone product of the PKS genes. Roles for spnF and spnL in the formation of carbon-carbon bridges are consistent with their similarities to enzymes that methylate carbon atoms (Table 11). The absence of partially modified intermediates in the blocked mutants may result from instability of the compounds, or from reduced biosynthesis due to lack of glycosylated molecules to act as positive regulators, analogous to those of the tylosin pathway (Fish & Cundliffe, 1997).

spnG, spnH, spnI, spnK

Disruption of spnG also prevented spinosyn production, but the mutant strain could not bioconvert aglycone so this gene is required for a later step in the pathway (Table 12). Its sequence similarity to known glycosyl transferase genes (Table 11) suggests that spnG encodes the rhamnosyl transferase required for addition of the first sugar to the aglycone. The mutant with a disrupted spnG also lacked a functional 4′-O-methyltransferase (OMT) because it converted the 3′,4′-didesmethyl spinosyn (P) to the 4′-desmethyl spinosyn (K), but not to the fully methylated spinosyn A. The 4′-OMT activity was presumably not expressed in the mutant because the encoding gene (spnH) lies downstream of the disrupting integration in the same operon. The existence of this operon was confirmed by disrupting BamH1 fragment T, which spans the junction between spnG and spnH but is not internal to any open reading frame. Nevertheless, its disruption altered spinosyn synthesis, so this fragment must be internal to a single transcript that encompasses both genes. In addition to the expected loss of 4′-OMT activity encoded by spnH, this disruption also caused the unexpected loss of 3′-OMT function, leading to accumulation of spinosyn P (Table 12). The 3′ OMT activity appears to be encoded by the convergent downstream gene, spnI. This gene has most sequence similarity to the ORF Y gene of Streptomyces nogalator (Table 11). The function of the ORF Y product is unknown, but the organism produces an unusual tetra-methylated deoxysugar (nogalose) that is similar to the tri-methylated rhamnose of spinosyn A, so presumably both genes are involved in sugar methylation. Consistent with this hypothesis, disruption of spnI created a mutant that bioconverted spinosyn P only to the 3′-desmethyl spinosyn (J), not spinosyn A (Table 12). The disruption prevented any spinosyn accumulation in unsupplemented fermentations. spnK has a sequence similar to spnI and ORF Y, and presumably encodes the 2′-OMT. Its disruption also prevented accumulation of any spinosyns in unsupplemented fermentations (Table 12).

spnN, spnO, spnP

Disruption of genes spnN, spnO and spnP led to accumulation of the pseudoaglycone (Table 12). These genes are therefore involved in the biosynthesis or addition of the forosamine sugar. The similarity of spnP to glycosyl transferases (Table 11) indicates that it encodes the spinosyn forosamyl transferase. The high degree of similarity between spnO and a 2,3 dehydratase (Table 11) indicates that it is involved in the 2′-deoxygenation step of forosamine synthesis.

Rhamnose Genes

The overlapping inserts cloned in cosmids 9A6, 3E11 and 2C10 do not contain genes that encode the four enzymes required to produce rhamnose from glucose (Liu & Thorson, 1994). The first enzyme is a glucose thymidylate transferase (gtt), or equivalent enzyme, that activates glucose by addition of a nucleotidyl diphosphate (NDP). The second is a glucose dehydratase (gdh) to produce NDP-4-keto-6-deoxy-glucose, an intermediate common to many deoxysugar biosynthetic pathways. An epimerase (epi) and a ketoreductase (kre) specific for rhamnose synthesis are also required, to convert the NDP-4-keto-6-deoxy-glucose to NDP-L-rhamnose, the activated sugar that is the substrate of the glycosyltransferase adding rhamnose to the aglycone. Genes that code for these enzymes in S. spinosa were cloned from a separate library of 7–12 kb partial Sau3A I fragments in the λ vector ZAP Express™ (Stratagene, LaJolla, Calif.). Radiolabelled probes were prepared by random primer extension (Boehringer Mannheim, Indianapolis, Ind.) of fragments from plasmid pESC1 containing the Saccharopolyspora erythraea gdh (Linton et al., 1995) and gtt genes. Plaque hybridizations to screen the phage library were performed with a stringent wash of 0.5×SSC, 0.1%SDS at 65° C. for 1 h. The plasmid (pDAB1620 and pDAB1621) portions of the vector containing inserts were excised from two of the three hybridizing phage, and partially sequenced using Prism-Ready Sequencing Kits (ABI) and multiple primers. The sequenced part of the insert in pDAB1620 (SEQ ID NO: 25) includes an ORF that would encode a 329-amino acid polypeptide (SEQ ID NO:26) with 82% identity to the gdh product of S. erythraea. Adjacent to this gene is an ORF coding for a 275-amino acid polypeptide (SEQ ID NO:27) with 72% identity to the S. erythraea kre gene product. The sequenced part of the insert in pDAB1621 (SEQ ID NO: 28) contains an ORF encoding a 261-amino acid polypeptide (SEQ ID NO: 29) with 83% identity to the S. erythraea gtt gene product. A second probe for rhamnose genes was prepared by PCR amplification of S. spinosa genomic DNA using degenerate oligonucleotide primers (SEQ ID NO: 30 and SEQ ID NO: 31) based on conserved amino acid regions in known epi proteins (Jiang et al., 1991; Linton et al., 1995). PCR reactions were performed in a GeneAmp 9600 Thermocycler with AmpliTaq polymerase (Perkin-Elmer) using 30 cycles of 30 sec at 94° C., 30 sec at 60° C. and 45 sec at 72° C. The probe hybridized to one phage in the 7–12 kb library; the plasmid portion of the vector containing this insert (pDAB1622) was excised and partially sequenced (SEQ ID NO:32). It includes an ORF for a 202-amino acid polypeptide (SEQ ID NO:33) with 57% homology to the S. erythraea epi protein. The genes were disrupted by recombination with plasmids containing internal fragments (bases 382–941 in SEQ ID NO: 25, 1268–1867 in SEQ ID NO:25, 447–994 in SEQ ID NO:28 or 346–739 in SEQ ID NO:32). Apramycin-resistant exconjugants were obtained in all cases, but they were only capable of growth on osmotically-stabilized media such as CSM supplemented with sucrose at 200 g/L, or R6 (Matsushima et al., 1994). Even under these conditions, they grew much slower than the parent S. spinosa (NRRL 18395), and were morphologically distinct, with highly fragmented mycelia. These results could be due to the presence of rhamnose in the cell wall in S. spinosa and a requirement that these four genes be present for normal cell wall synthesis in this organism. Mutants disrupted in these genes grew too slowly to be fermented under conditions known to produce spinosyns. However, Southern hybridizations of S. spinosa genomic DNA with the S. erythraea gtt/gdh probe (washed in 2×SSC, 0.1%SDS at 65° C. for 1 h) or with the degenerate epi probe (washed in 0.1×SSC, 0.1% SDS at 65° C. for 1 h) indicated that there are no other homologues of these genes present in the S. spinosa genome. Therefore, the four cloned S. spinosa genes must be the sole source of rhamnose for both cell wall formation and spinosyn biosynthesis.

The nucleotide sequence and corresponding amino acid sequence for each of the four S. spinosa genes required to produce rhamnose are identified in the following Table 13:

TABLE 13 gene DNA sequence amino acid sequence S. spinosa gtt SEQ ID NO:28, bases 334–1119 SEQ ID NO:29 S. spinosa gdh SEQ ID NO:25, bases 88–1077 SEQ ID NO:26 S. spinosa epi SEQ ID NO:32, bases 226–834 SEQ ID NO:33 S. spinosa kre SEQ ID NO:25, bases 1165–1992 SEQ ID NO:27

Thus 23 genes from S. spinosa can be assigned roles in spinosyn biosynthesis: 5 PKS genes to produce a macrocyclic lactone, 4 genes to modify this to the aglycone, 5 genes to synthesize and add rhamnose, 3 genes to methylate the rhamnose, and 6 genes to synthesize and add forosamine. The hypothetical biosynthetic pathway is summarized in FIG. 1.

Utility

There are many uses for the cloned Saccharopolyspora spinosa DNA. The cloned genes can be used to improve yields of spinosyns and to produce new spinosyns. Improved yields can be obtained by integrating into the genome of a particular strain a duplicate copy of the gene for whatever enzyme is rate limiting in that strain. In the extreme case where the biosynthetic pathway is blocked in a particular mutant strain due to lack of a required enzyme, production of the desired spinosyns can be restored by integrating a copy of the required gene. Yield improvement obtained by integrating copies of spinosyn genes is illustrated hereinafter in Examples 1–3 and 6.

Novel spinosyns can be produced using fragments of the cloned DNA to disrupt steps in the biosynthesis of spinosyns. Such disruption may lead to the accumulation of precursors or “shunt” products (the naturally-processed derivatives of precursors). The fragments useful in carrying out disruptions are those internal to a gene with bases omitted from both the 5′ and 3′ ends of the gene. Homologous recombination events utilizing such fragments result in two partial copies of the gene: one that is missing the omitted bases from the 5′ end and one that is missing the omitted bases from the 3′ end. The number of bases omitted at each end of the fragment must be large enough so that neither of the partial copies of the gene retains activity. At least 50 bases will normally be omitted from each end, and more preferably at least 100 bases are omitted from each end. The length of the partial gene fragment should be large enough so that recombination frequency is high enough for a practical experiment. Useful fragments for disruptions are desirably at least 300 bases long, and more preferably at least about 600 bases long. Modified spinosyns produced by disrupting genes may be insect control agents themselves, or serve as substrates for further chemical modification, creating new semi-synthetic spinosyns with unique properties and spectra of activity. Example 4 hereinafter illustrates the use of disruption.

Novel spinosyns can also be produced by mutagenesis of the cloned genes, and substitution of the mutated genes for their unmutated counterparts in a spinosyn-producing organism. Mutagenesis may involve, for example: 1) deletion or inactivation of a KR, DH or ER domain so that one or more of these functions is blocked and the strain produces a spinosyn having a lactone nucleus with a double bond, a hydroxyl group, or a keto group that is not present in the nucleus of spinosyn A (see Donadio et al., 1993); 2) replacement of an AT domain so that a different carboxylic acid is incorporated in the lactone nucleus (see Ruan et al., 1997); 3) addition of a KR, DH, or ER domain to an existing PKS module so that the strain produces a spinosyn having a lactone nucleus with a saturated bond, hydroxyl group, or double bond that is not present in the nucleus of spinosyn A; or 4) addition or subtraction of a complete PKS module so that the cyclic lactone nucleus has a greater or lesser number of carbon atoms. Example 5 illustrates use of mutagenesis to produce a spinosyn with modified functionality.

The DNA from the spinosyn gene cluster region can be used as a hybridization probe to identify homologous sequences. Thus, the DNA cloned here could be used to locate additional plasmids from the Saccharopolyspora spinosa gene libraries which overlap the region described here but also contain previously uncloned DNA from adjacent regions in the genome of Saccharopolyspora spinosa. In addition, DNA from the region cloned here may be used to identify non-identical but similar sequences in other organisms. Hybridization probes are normally at least about 20 bases long and are labeled to permit detection.

The modified strains provided by the invention may be cultivated to provide spinosyns using conventional protocols such as those disclosed in U.S. Pat. No. 5,362,634.

The following examples are provided in order that the invention might be more completely understood. They should not be construed as limitations of the invention.

EXAMPLE 1 Improved Yield of Spinosyns A and D by Transformation with Cosmid 9A6

Vegetative cultures of S. spinosa strain NRRL18538 were grown in 50 ml CSM medium (trypticase soy broth 30 g/l, yeast extract 3 g/l, magnesium sulfate 2 g/l, glucose 5 g/l, maltose 4 g/l) in 250 ml Erlenmeyer flasks shaken at 300 rpm at 30° C. for 48 h. Fermentation cultures contained a 1 ml inoculum of this vegetative culture in 7 ml of INF202, a proprietary medium similar to that described in Strobel & Nakatsukasa (1993). The cultures were grown in 30 ml plastic bottles arranged in 10×10 modules, shaken at 300 rpm in a 30° C. room for 3, 5 or 7 days. Broths were extracted with 4 volumes of acetonitrile, then analyzed for spinosyns A+D by isocratic high pressure liquid chromatography (HPLC) through a C-18 reversed-phase column (Strobel and Nakatsukasa, 1993). The amount of spinosyns was determined from absorbance at 250 nm. For each time point, spinosyns A+D were determined from 10 fermentation bottles. Two representative samples from each set of replicates were also analyzed by a slightly modified HPLC system for pseudoaglycone (PSA), the spinosyn precursor which lacks forosamine. In this system the mobile phase is 35:35:30 acetonitrile/methanol/0.5% (w/v) aqueous ammonium acetate (R. Wijayaratne, unpublished).

The cultures contain not only the insect-active spinosyns A and D, but also pseudoaglycone (Table 14).

TABLE 14 Spinosyn production in strain NRRL 18538 Time A + D (μg/ml) PSA (μg/ml) 3 d 101 ± 3  109 ± 11 5 d 269 ± 14 155 ± 26 7 d 334 ± 32 110 ± 53 The values are means ± 95% confidence levels. The accumulation of the pseudoaglycone, a forosamine-deficient precursor of spinosyn A, suggests that, in this strain grown under these conditions, the yield of spinosyns A+D is limited by the supply and/or addition of forosamine

Cosmid 9A6 was conjugated from E. coli strain S17-1 (Simon et al., 1983) into S. spinosa strain NRRL 18538 using the method of Matsushima et al. (1994). Six independent isolates transformed with Cosmid 9A6 were subsequently grown and analyzed for spinosyn factor production under the fermentation conditions described above. The average yield of spinosyns A+D from these strains was higher than from their parent, by 35 μg/ml after 3 days of fermentation, and by 37 μg/ml after 5 days. The amount of pseudoaglycone in the transformed cultures was lower than in the parent strain throughout the fermentation (Table 15)

TABLE 15 Spinosyn production in derivatives of NRRL 18538 transformed with Cosmid 9A6. Time A + D (μg/ml) PSA (μg/ml) 3 d 136 ± 4 31 ± 2  5 d 306 ± 5 7 ± 2 7 d 365 ± 7 7 ± 1 The values are means ± 95% confidence levels.

Strain NRRL 18538 and 6 independent isolates transformed with Cosmid 9A6 were analyzed for spinosyn content at different times during fermentation. For each strain, spinosyns A+D were determined from 10 fermentation bottles (Table 16). Two samples from each set of replicates were also analyzed for pseudoaglycone content (Table 17).

TABLE 16 Effect of Cosmid 9A6 on spinosyn A + D in NRRL 18538 Time −9A6 +9A6 Effect of 9A6 3 d 101 ± 3  136 ± 4 +35% 5 d 269 ± 14 306 ± 5 +14% 7 d 334 ± 32 365 ± 7  +9% 9 d 414 ± 17 411 ± 8  −1% The values are means in μg/ml ± 95% confidence levels.

TABLE 17 Effect of Cosmid 9A6 on pseudoaglycone accumulation in NRRL 18538 Time −9A6 +9A6 Effect of 9A6 3 d 109 ± 11 31 ± 2  −72% 5 d 155 ± 26 7 ± 2 −95% 7 d 110 ± 53 7 ± 1 −94% 9 d 119 ± 11 5 ± 1 −96% The values are means in μg/ml ± 95% confidence levels.

It has therefore been demonstrated that transformation with Cosmid 9A6 can improve the efficiency with which precursor pseudoaglycone is processed to spinosyns. In NRRL 18538, the yield improvements for spinosyn A+D were 35% after 3 days of fermentation, and 14% after 5 days (Table 15). The rate-limiting process appears be the supply and/or addition of forosamine because pseudoaglycone was present in the parent at about 120 μg/ml throughout the fermentation, but in the transconjugants it was reduced to about 30 μg/ml at 3 days, and essentially depleted thereafter (Table 15). Although the conversion was not quantitative, the data are consistent with an improved efficiency in the processing of pseudoaglycone to spinosyn A+D in strains transformed with Cosmid 9A6. The effect could be the result of duplicating a forosamine biosynthetic gene, a forosaminyltransferase gene, or a combination of improvements. There was no statistically significant difference between the spinosyn A+D yields from the NRRL 18358 strains with or without Cosmid 9A6 after 7 or 9 days fermentation. Pseudoaglycone was still reduced in the transconjugants, but the extra spinosyn A+D produced by its conversion may not have been detectable against the higher background of spinosyns accumulated by this stage of the fermentation.

EXAMPLE 2 Correction of Methylation Deficiencies in Strain NRRL 18823 by Cosmid 9A6

Although spinosyn synthesis is limited by forosamine supply/addition in strain NRRL 18358, other biosynthetic functions may be limiting in other strains. S. spinosa strain NRRL18823 accumulates spinosyn H (2′-desmethyl-spinosyn A; Kirst et al., 1992), rather than spinosyn A. Spinosyn H is not an intermediate in the spinosyn A biosynthetic pathway, but a “shunt” product synthesized naturally when 2′-O-methylation does not occur. Cosmid 9A6 was conjugated from E. coli strain S17-1 into strain NRRL 18823 using the method described above. Two of the resulting exconjugants, when fermented, produced predominantly spinosyn A, with little spinosyn H (Table 18).

TABLE 18 Strain H (μg/ml) A + D (μg/ml) NRRL 18823 323 0 NRRL 18823/9A6-2 36 551 NRRL 18823/9A6-5 45 646 This shows that transformation with Cosmid 9A6 is able to overcome a second type of limitation to spinosyn production—the methylation deficiency in strain NRRL 18823.

EXAMPLE 3 Correction of 4′-O-methylation Deficiency in Strain NRRL 18743 by Cosmid 9A6

S. spinosa strain NRRL18743 accumulates spinosyn K (4′-desmethyl-spinosyn A), an intermediate in the spinosyn A biosynthetic pathway. Two of the exconjugants of strain NRRL 18743 containing Cosmid 9A6 produced predominantly spinosyn A, with little spinosyn K, while the third produced no detectable spinosyn K (Table 19).

TABLE 19 Strain K (μg/ml) A + D (μg/ml) NRRL 18743 488 0 NRRL 18743/9A6-1 38 829 NRRL 18743/9A6-2 22 725 NRRL 18743/9A6-3 0 706 This demonstrates that transformation with Cosmid 9A6 is able to overcome a third type of limitation to spinosyn A production—the methylation deficiency in strain NRRL 18743.

EXAMPLE 4 Accumulation of Spinosyn Precursor Caused by Disruption of spnP

An internal fragment of spnP (bases 7391–8159) was amplified in a polymerase chain reaction using primers given in SEQ ID NO:34 and SEQ ID NO:35. AmpliTaq polymerase (Perkin Elmer, Foster City, Calif.) was used according to the manufacturer's instructions, in a 100 μl reaction with 20 pmoles of each primer and 1 μg of 9A6 DNA. The mixture was subjected to 25 cycles of 60 sec at 94° C., 60 sec at 37° C. and 120 sec at 72° C. The amplification product was cloned as an EcoR1-HindIII fragment into the plasmid vector pOJ260 (Bierman et al., 1992), then conjugated from E. coli S17-1 into S. spinosa NRRL 18538. Stable exconjugants, resulting from a single homologous recombination event between the plasmid-born and chromosomal sequences, contain a copy of the vector DNA integrated into the chromosome between two incomplete copies of spnP. When fermented, these exconjugants accumulate the forosamine-deficient precursor pseudoaglycones, rather than the end products spinosyns A and D (Table 20).

TABLE 20 Strain PSA (μg/ml) A + D (μg/ml) NRRL 18538 79 284 NRRL 18538/1614-2 416 22 NRRL 18538/1615-1 372 21 NRRL 18538/1615-2 543 21 NRRL 18538/1615-5 476 19 NRRL 18538/1615-6 504 18 The pseudoaglycones are intermediates useful in the preparation of known insecticides (International Application WO 93/09126)

EXAMPLE 5 Accumulation of a Novel Spinosyn Following Modification of the PKS Domain ER2

Overlapping, complementary oligonucleotides SEQ ID NO: 36 and SEQ ID NO: 37 were designed to modify the gene encoding the enoyl reductase function in module 2 of the spinosyn PKS. These mutagenic primers provide for substitution of the sequence TCACC in place of GGTGG at bases 33563–33567 of SEQ ID NO:1, so that the sequence encodes a serine-proline dipeptide instead of a glycine-glycine dipeptide in the putative NAD(P)H-binding motif A similar substitution was successfully used to inactivate an erythromycin ER without affecting any other PKS functions (Donadio et al., 1993). The substitution simultaneously introduced a novel PinA1 restriction site, and eliminated a SgrA1 site, to facilitate detection of the engineered DNA in recombinant organisms.

In the first step of the mutagenesis, two separate PCR amplifications were performed, one using the mutagenic primer SEQ ID NO: 36 and flanking primer SEQ ID NO: 38, the other using mutagenic primer SEQ ID NO: 37 and flanking primer SEQ ID NO: 39. In the second step, the products of the first reactions were diluted 100-fold, pooled and amplified with only the flanking primers SEQ ID NO: 38 and SEQ ID NO: 39. In the third step, the products of the second PCR reaction were cloned into the plasmid pCRII according to the manufacturer's instructions (InVitrogen, San Diego, Calif.). A portion of the mutated ER2 domain (spanning bases 33424–33626 in SEQ ID NO: 1) was excised as a Van911-NheI fragment, and inserted in place of the wild-type Van911-NheI fragment in a 3.5 kb EcoR1 fragment of cosmid 3E11 (bases 32162–35620 in SEQ ID NO: 1) cloned in the plasmid pBluescript SK-(Stratagene). The mutated EcoR1 fragment was then transferred into the conjugative plasmid pDAB1523 (FIG. 5), a derivative of pOJ260 containing the rpsL gene of Streptomyces roseosporus that confers a counter-selectable streptomycin-sensitive phenotype (Hosted & Baltz, 1997). The resultant plasmid containing the mutated EcoR1 fragment was conjugated from E. coli S17-1 (Simon et al., 1983) into SS15, a spontaneous streptomycin-resistant derivative of S. spinosa strain NRRL18538, using the method of Matsushima et al. (1994). (Spontaneous streptomycin-resistant derivatives of S. spinosa strain NRRL18538 can be readily isolated by those skilled in the art.) Apramycin-resistant exconjugants were shown to contain both wild-type and mutated versions of the ER2 domain by Southern hybridization with digoxygenin-labeled probes (Boehringer Mannheim). They also contained the S. roseosporus rpsL gene and consequently, on BHI agar (Difco, Detroit, Mich.) containing streptomycin at 150 mg/L, they grew poorly and failed to produce aerial mycelium. Spontaneous revertants to streptomycin-resistance were selected on the basis of their ability to grow and produce white, aerial mycelium on BHI agar containing streptomycin at 150 mg/L. Southern analysis indicated that these strains no longer contained the S. roseosporus rpsL gene or any other pDAB1523 sequences. Some strains had lost the entire cluster of spinosyn biosynthetic genes, including the ER2 domain, as well as pDAB1523. In other strains the pDAB1523 sequences had been excised along with the mutant ER2 domain, re-creating the parental gene structure. In a third type of streptomycin-resistant strain, the pDAB1523 had been excised with the wild-type ER2 domain, leaving the mutated version in its place. When fermented, a strain of this third type produced a novel metabolite, separable from spinosyn A by liquid chromatography on a C18 column (ODS-AQ, YMC, Wilmington, N.C.) using a mobile phase of acetonitrile: methanol: 2% ammonium acetate (44:44:12). The new entity was analyzed by electrospray ionization and tandem mass spectroscopy (Balcer et al., 1996) using a triple quadrupole mass spectrometer (TSQ700, Finnigan MAT, San Jose, Calif.). It had the properties expected of the C18:C19-anhydrospinosyn A, with a mass of 729.5 daltons and produced the 142 dalton forosamine fragment. We conclude that modification of DNA encoding PKS domains results in the production of novel fermentation products.

EXAMPLE 6 Improved Yield of Spinosyns A and D by Transformation of NRRL 18538 with Rhamnose Biosynthetic Genes

Fragments containing the rhamnose biosynthetic genes were cloned independently into the conjugative vector pOJ260 (Bierman et al., 1992). The resulting plasmids are listed in Table 21.

TABLE 21 Plasmid Genes pDAB1632 gtt pDAB1634 gdh + kre pDAB1633 epi

Each plasmid was conjugated from E. coli S17-1 (Simon et al., 1983) into S. spinosa NRRL 18538 by the method of Matsushima et al. (1994). Apramycin-resistant exconjugants, presumably containing a plasmid integrated into the chromosome by homologous recombination, were selected and fermented (Table 22).

TABLE 22 Spinosyn production in derivatives of NRRL 15328 transformed with rhamnose genes Duplicated A + D (μg/ml) Strain Genes Experiment 1 Experiment 2 NRRL 18538 None 344 ± 39 405 ± 25 NRRL 18538/1632-1 gtt 410 ± 21 418 ± 38 NRRL 18538/1634-1 gdh + kre 351 ± 27 360 ± 21 NRRL 18538/1633-1 epi 318 ± 29 315 ± 18 The values are means ± 95% confidence limits.

In derivatives of NRRL 15328 transformed with gtt or epi, or the combination of gdh and kre, there was no consistent increase in the yield of spinosyns.

The fragments containing the gtt and gdh+kre genes were combined in a single plasmid. Two plasmids containing the combined gtt, gdh and kre genes (pDAB1654 and pDAB1655) were isolated, and conjugated from E. coli S17-1 (Simon et al., 1983) into S. spinosa NRRL 18538 by the method of Matsushima et al. (1994). Apramycin-resistant exconjugants were selected and fermented (Table 23).

TABLE 23 Spinosyn production in derivatives of NRRL 15328 transformed with rhamnose genes Duplicated A + D (μg/ml) Strain Genes Experiment 1 Experiment 2 NRRL 18538 None 109 ± 9  133 ± 36 NRRL 18538/1654-2 gtt, gdh and kre 323 ± 19 244 ± 34 NRRL 18538/1654-5 gtt, gdh and kre 571 ± 23 412 ± 61 NRRL 18538/1654-6 gtt, gdh and kre 577 ± 17 425 ± 51 NRRL 18538/1654-11 gtt, gdh and kre 587 ± 23 426 ± 55 NRRL 18538/1655-1 gtt, gdh and kre 501 ± 20 395 ± 59 NRRL 18538/1655-3 gtt, gdh and kre 537 ± 27 421 ± 63 NRRL 18538/1655-5 gtt, gdh and kre 529 ± 21 428 ± 47 NRRL 18538/1655-12 gtt, gdh and kre 526 ± 26 401 ± 60 The values are means ± 95% confidence limits.

In derivatives of NRRL 15328 transformed with the gtt, gdh and kre genes, significant increases in spinosyn yields were observed. This probably results from overcoming a rate-limiting supply of NDP-4-keto-6-deoxy-glucose by simultaneously increasing the amounts of both gtt and gdh gene products, the enzymes necessary for its biosynthesis (see FIG. 1). A greater supply of the NDP-4-keto-6-deoxy-glucose intermediate would lead to increased production of both rhamnose and forosamine, and therefore greater ability to convert aglycone to spinosyns A+D. Consistent with the hypothesis that deoxysugar supply is limiting spinosyn production in NRRL 18538, many mutants blocked in forosamine synthesis or addition accumulate PSA to very high levels. More of this intermediate can be made because it requires only one deoxysugar, compared with the two required for spinosyns A or D.

The present invention is not limited to a particular vector comprising spinosyn genes of the invention, but rather encompasses the biosynthetic genes in whatever vector is used to introduce the genes into a recombinant host cell.

In addition, due to the degeneracy of the genetic code, those skilled in the art are familiar with synthetic methods of preparing DNA sequences which may code for the same or functionally the same activity as that of the natural gene sequence. Likewise, those skilled in the art are familiar with techniques for modifying or mutating the gene sequence to prepare new sequences which encode the same or substantially the same polypeptide activity as the natural sequences. Consequently, these synthetic mutant and modified forms of the genes and expression products of these genes are also meant to be encompassed by the present invention.

All patents and publications referred to above are incorporated by reference herein.

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1. An isolated DNA molecule comprising a DNA sequence that encodes the spinosyn biosynthetic enzyme spnF, wherein said enzyme is defined by the amino acid sequence SEQ ID NO:
 7. 2. An isolated DNA molecule of claim 1 wherein said DNA sequence is bases 20168–20995 of SEQ ID NO:1.
 3. A recombinant DNA vector which comprises a DNA sequence as defined in claim
 1. 4. A host cell transformed with a recombinant vector as claimed in claim
 3. 5. A process for isolating a macrolide biosynthetic gene which comprises a) creating a genomic library of a macrolide producing microorganism, and b) using a labeled DNA molecule according to claim 1 as a hybridization probe.
 6. A process of claim 5 wherein the microorganism is a spinosyn producing microorganism. 